Walking after you
by pegasus-fics
Summary: [COMPLETE] When John’s team goes off world on a routine mission, they reunite with an old friend. SPOILERS FOR SEASON 4! Completed!
1. Chapter 1

**Title:****Walking After You**  
**Summary:** When John's team goes off world on a routine mission, they reunite with an old friend.  
**Genre:** drama, romance, angst  
**Pairings:** Elizabeth/John  
**Main characters:** Elizabeth, John  
**Rating: **PG-13  
**Warnings: **none

**Spoilers: all of season 4, mainly events from Adrift and Lifeline but spoilers and speculations throughout. If you don't want to be spoiled, don't read.**

**Disclaimer: **Stargate Atlantis and it's characters don't belong to me.  
**A/N:** This one is set at the end of season 4, kind of like I'd like the show to end if it ended in season 4.  
**A/N2**: Title taken from the beautiful song by Foo Fighters.

Huge thanks goes to jackfan2 for the beta!

* * *

John Sheppard's team stepped through the gate to MR7-247 and took in their surroundings. The planet was beautiful; the sun was shining brightly high in the sky, all around them sounded the chirping of birds and crickets in the lush grass and they could hear the bubble of a nearby creek. The Stargate stood on a huge clearing and there were hills around them as far as the eye could see.

With a smile, Colonel Sheppard took the lead and donned his sunglasses. Without looking back, he called to his team, "Ok guys, let's go and see what this planet is like."

They made their way down the path that lead away from the Stargate, going through a valley next to the stream, their postures were relaxed but alert at the same time. To their surprise the trail led them to a beautiful small town with a well in the middle of a square, simple houses and several markets surrounding it. They smiled as the people around them passed by, nodding their heads in greeting. The villagers looked at the strangers curiously but didn't appear to be afraid of them.

John approached a small grocery market, his eyes scanning the goods laid out on one table. He smiled at the seller and asked, "Hello, we were wondering if we could talk to the leader of your people. We are interested in trade."

"Of course, Maya here will show you the way to the town hall." The seller ushered his young assistant and the team went obediently after her, but not before Rodney had a chance to pick and buy some kind of green fruit to satisfy his growling stomach.

They were led to the town hall, a single stone building taller than the rest, the town's flag and name put up proudly on the front; Erentria. Maya led them inside up to the first floor, knocking on the door there.

"Come in." Maya entered shyly and the team followed her.

"Councilor, I am sorry to disturb you, these people wanted to talk to you." The councilor smiled at the young woman.

"Thank you, Maya. You may go." He stood up from his desk and went around it to greet the team as Maya scurried out of the room, closing the door behind her. He was around forty years old, his hair was raven black, his eyes piercing blue and he had a beard.

"Welcome to Erentria, my name is Durai and I am the leader of this town." He smiled at the strangers and bowed his head.

"Lt. Colonel John Sheppard, Dr. Rodney McKay, Major Evan Lorne and Ronon Dex. We are pleased to meet you." John smiled back as he introduced his team.

"So," Durai smiled and sat on the front edge of his desk, "what brings you here to our little town?" He motioned them to sit down; muttering their thanks, John and Rodney took the seats in front of Durai's desk while Lorne and Ronon sat on a small sofa on one side of the room.

"We are looking for allies and trading partners if you are willing."

The councilor seemed to ponder this a moment before asking, "What do your people wish to trade, Colonel?"

"Our allies offer us a portion of their crops when the harvest season comes, in turn we provide them medical supplies, man power when needed and protection from the Wraith." John watched as utter anguish passed over Durai's face but was quickly replaced.

"Yes, that would be wonderful. Although we have heard that it seems the Wraith's numbers are diminishing. The last culling here was a year ago, many of my people were taken that day."

"I'm sorry to hear that, Durai."

"Where are you from?"

"We're from Alterran." Durai's head snapped up at Rodney's response.

"Alterran? Really? Our ancestors were friends with the Alterran people but after the war my ancestors haven't heard from them."

"They were forced to leave to another planet and settled there. We're their...descendants." Rodney replied.

"And you can really help us fight the Wraith?" Durai asked rather skeptically.

"Well, we will try our best." John smiled at him reassuringly.

"I'm sure my people will be glad for new friends. We shall discuss the details later; I guess you must be tired; the trek from the Ring is long. Why don't you dine with me and my family?" Ronon and Rodney's head shot up at the mention of food and John and Lorne rolled their eyes.

"If it's not a problem for you; we don't like to bother."

"Nonsense, Colonel. Please follow me, I will ensure myself you have rooms ready for your stay."

"Thank you, Durai." They followed him out and to the town square again.

"I will let the cook know we will have guests, meanwhile," Durai waived one arm to indicate the small town, "feel free to look around." John smiled and nodded as the councilor left them to do just that.

Rodney polished the fruit he bought earlier with his sleeve and bit into it, surprised at its rich flavor. "Hmm, that's good. We should take some with us back to Atlantis."

"Later Rodney. Lorne, looks like we'll be staying overnight, get back to the gate and report to Colonel Carter."

"Yes, sir." The Major nodded and left, smiling as he saw two women looking at him with interest.

Adopting a casual air, John pivoted to survey the town with a careful eye. It looked much like the towns in Western movies but the surrounding buildings were made mainly of stone. With his back now to the astrophysicist, he heard as Rodney continued to munch happily on the fruit he'd purchased.

With his back turned, John failed to see Rodney become deathly still. McKay's eyes went wide and the cherished fruit, suddenly forgotten, slipped carelessly from his hand to land with a thunk on the dusty street. Stunned to silence, Rodney's mouth now hung open in an uncharacteristic loss for words.

With his back turned, John also failed to notice Rodney's gaze locked straight ahead. One arm shot out, reaching back blindly, patting the air behind him in a near panic, reaching for Sheppard's back, desperate for his attention. It wasn't until McKay's hand found it's target and the persistent tapping got the desired effect.

"What is it?" John asked, his own gaze fixed on two men arguing lightly at a nearby fruit stand. The tapping continued, more fervently, incessantly… annoyingly. "McKay, what?" The lack of verbal response, coupled with the now physical slaps to his person, irritated the colonel and he rounded on the scientist, teeth clenched, "Rodney, how many times do I have to tell you-"

Rodney's wide, terrified eyes brought John up short. The scientist's hand was now clenching at John's collar and the other was raised, pointing to a place straight ahead. Nervously, John licked his lips as his gaze trailed in that direction and he froze. Ronon's hand reached for his gun but John stopped him.

There, leaning in the doorway of one house, was Elizabeth Weir, watching them quietly.

**TBC**


	2. Chapter 2

His feet obviously had a mind of their own as they led him towards her, albeit hesitantly, not knowing what to expect.

"Elizabeth?" He said softly and licked his dry lips.

"John." She said his name just as softly and looked into his eyes. He wanted to hug her so badly but couldn't risk it, knowing what she became and what she could do. He heard Ronon and Rodney move to his side. "Rodney. Ronon."

It's been a year since they last saw her, since they had to leave her on the Asuran home world. Everyone thought she was dead but John never lost hope of finding her alive, though lately his hope was fading away with each mission they went on and coming up empty-handed. But now, now she was standing in front of him, dressed in long brown skirt and white blouse, her hair falling to her shoulders in rich curls.

"I thought you were dead." Rodney stated by way of greeting and John felt like punching him.

"I managed to escape after they started attacking the Wraith."

"Are you okay?"

Elizabeth nodded and smiled. "I'm fine, Rodney."

"So you've been here for a year now?" Rodney kept asking questions while John just stood there, looking at her. She was beautiful, just like he remembered.

"Yes."

"Why didn't you come back home?"

"Well, for one, I didn't know the new coordinates and even if I did I figured my IDC wouldn't be valid by the time I managed to escape."

"True."

"Ah, there you are, Colonel." Durai interrupted, "I was looking for you. I see you are already trying to charm the lady here." Elizabeth chuckled and shook her head.

"It's okay, Durai, they're my friends. Their charms don't work at me." Seeing John pout she tried to keep herself from laughing.

"Really? What a small world."

"Try galaxy." Rodney mumbled and behind him Ronon smirked.

"Elizabeth, would you like to join us for dinner?" At Durai's question, the team looked at her expectantly.

"I don't want to intrude..." She said hesitantly.

"So that's a yes, then." Durai smiled mischievously and Elizabeth rolled her eyes. "I'm going to help my wife, if you'll excuse me." Durai walked off, leaving Elizabeth with the team.

"Ma'am?" She heard the sound to her right and turned. Major Lorne was now making his way back to his teammates.

"Major! It's nice to see you again. Where's Teyla?"

"She's in Atlantis with the baby." Rodney replied inadvertently.

"Baby?!" Elizabeth turned back to face McKay. Teyla with a baby? Her mind was filled with so many questions.

"It's a long story." John replied with a wince and Elizabeth studied him. Was he the father?

"Sir," Lorne continued, never quite looking away from Elizabeth for long, "Colonel Carter says we don't need to hurry and that we should enjoy ourselves."

"Colonel Carter?"

"That's a long story too." John grinned and shrugged. They turned when they heard Durai call them for dinner and followed.

"It was really bad, I lost my sister. But if it wasn't for Elizabeth here, the whole village would be non-existent today." Said Durai with proud look on his face while they were dining.

John, sitting opposite Elizabeth, just stared at her in awe; he could see she was blushing and kept her eyes on her soup, stirring it around in the pot. Soon the group was chatting with Durai and his family like long lost friends. After all food was eaten, Durai noticed it was fairly late.

"I'm going to set you up in our finest hotel for the night, please excuse me..."

"Durai, that's not necessary." Elizabeth piped up and all heads turned to her. "I have plenty of room in the house."

"Very well, at least this way you can catch up." Durai smiled and clasped his hands. "Have a good night." He bowed and the team stood up and left, bidding Durai and his family goodnight. Elizabeth led them to her house.

"I'm beat." Rodney complained as they walked the short distance. Elizabeth smiled and let them in, giving them a small tour and assigning them their rooms.

"Whoa, wait. I'm not sleeping with Rodney in the same room." John complained and was on the receiving end of Rodney's death glare.

"Oh, and may I ask why?"

"You snore."

"I do not snore."

"Yes you do, McKay." Lorne confirmed; he had been on the receiving end of Rodney's snoring not long ago. Rodney folded his arms and his lips narrowed to thin line.

"Fine."

"It's okay, Rodney. If you don't mind John, you can sleep in the living room."

"Okay, thanks."

The team scattered around the house; Ronon, Rodney and Lorne walked upstairs to their respective rooms while John watched as Elizabeth busied herself with something in the kitchen.

"Can I use your shower? Uhm...if you have shower." Elizabeth chuckled at John's question.

"Go right ahead. And yes, I do have a shower. Try to be quick; I don't have unending supply of hot water."

"Yes, ma'am." He shucked off his vest and draped it over the kitchen chair, walking to the bathroom.

Elizabeth watched him go for a while and then moved to gather an extra pillow and quilt, setting them up on the living room couch. John emerged from the bathroom just as she was finishing up.

"There, all set." She smiled at him when he walked over to her, his hair still wet.

"Thanks, Elizabeth."

"You're welcome." She disappeared into her room for a moment and then went to the bathroom. Meanwhile John settled himself on the couch, his hands under his head as he listened to the sounds around him; the running shower, the chirping of crickets he could hear from the open window.

It wasn't long before Elizabeth finished her shower, and walking out of the bathroom a few minutes later, dressed in a short flowing top; John tried not to notice, so he shut his eyes but opened them when he heard Elizabeth's voice.

"Goodnight, John."

"Goodnight, Elizabeth."

After one hour of tossing and turning John decided it was futile to try to fall asleep. His body was tired but his mind was reeling with memories and feelings from the past year and before. When he closed his eyes again he heard the door from Elizabeth's bedroom open and then close. The house had a wooden floor and sometimes the floor would creak and he figured she walked on tip toes so she wouldn't wake him. He felt a soft rush of air as she passed by and he wondered what she was up to. Then he heard her open the back door and he shivered when the night cold air drafted through until the door was closed again. He opened his eyes and peeked over the sofa's back, scanning the room.

Sitting up, he untangled his legs from the quilt and put on his boots and uniform jacket and decided to follow her. He opened the door quietly and for a few moments and stood in the doorway, looking over a small patio and small backyard. However, what caught his eye first was Elizabeth, standing by the railing in the darkness, looking over the backyard and the sky, a large woolen shawl wrapped around her body. A sight that was so familiar, yet so different.

"Are you going to stand there all night?" Her voice shook him out of his thoughts and he tugged his jacket around him more tightly against the cold night air. After closing the door behind him, he stepped up beside her, propping his arms on the railing. She cast him a sideways glance and asked: "Did I wake you?"

"No." He shook his head, "Couldn't sleep. Too many things on my mind."

In the moonlight night, he studied her profile and the way her long hair caught the evening breezes. In the past year he never realized how much he missed her but now that she was standing beside him on another balcony, the realization hit him full force. He missed their talks, her smile, her laughter and her calming presence. True, during the year they all were busy fighting the Wraith and Asurans and often faced challenges and surprises, many of them unpleasant, so he rarely had the chance to reminisce.

Taking a deep breath, he started speaking. "Listen, I-" he paused when she looked at him then at his hand now resting on her shoulder; he didn't even realize he was reaching for her. There was a pause when he removed his hand.

"Let me guess, Rodney forbade you any contact." When he only nodded she added, "John, you know I would never hurt you, either of you."

"Yeah I know. But you know Rodney, he's-"

"He's afraid of me." She interrupted him and he wanted to argue but she stopped him. "It's okay, John. I realize that I have something inside me to be afraid of. Rodney has every right to fear me."

"Maybe, but you're still his friend. And he should worry about how to get you back instead of his own ass for a change."

"He can't."

"What do you mean?"

"It's not possible to remove the nanites without killing me."

"But there must be-"

"No." The silence stretched between them and John contemplated the information she just gave him. His chest tightened at the thought of finally finding her and then losing her again.

"What did you want to say?" She asked a few minutes later.

"Hmm?"

"Before."

"I wanted to thank you for saving our asses back there." A small sad smile spread across her face and she nodded.

"Anyone would do the same."

"Maybe, but you risked your life for us." He paused and watched her quietly. "I never gave up hope of finding you, Elizabeth." He said softly, quietly. Her head bowed and she closed her eyes as she remembered the day clearly, as it had been just yesterday. "Come here."

Her eyes lifted to meet his and she bit her lip nervously. She stepped closer to him and hesitated, until he put his arms around her shoulders, hugging her close. Her own arms circled his torso, holding on tight as her emotions threatened to spill. She tucked her head in the crook of his neck and sighed and he smiled, tightening his hold on her and pressing a kiss to the top of her head. He felt warm wetness on the side of his neck, felt her eyelashes flutter against his skin as she closed her eyes against the tears he couldn't see but could feel.

"If Rodney saw us right now," John said, his own voice husky with emotion, "he would throw a fit." When he finished with a smile, trying to lighten the mood, he was rewarded with the sound of her soft laughter.

"John?" She said and he could feel her breath on his neck; it made him shiver. "Thank you for not giving up on me." She sniffed and he held on.

The next day flew by quickly; the Atlantians sealed the trade deal with the Erentrians and gave them information about how to contact Atlantis in case they needed help. It was almost evening when Elizabeth, Durai and John's team approached the Stargate, ready to say their goodbyes.

Clasping Elizabeth's hand discreetly, John slowed, covertly allowing his team and Durai to go ahead. No one noticed them as they continued their quiet conversation with the councilor.

"Come back with us." John whispered to Elizabeth.

"You know I can't." She sighed sadly. "Once they know I'm alive and where I am, they will want to...extinguish me or use me as their guinea-pig."

"But if we tell them you're no danger to us..."

"They will never believe me...or you."

"So you want us to leave you out of our reports." She only nodded. "Okay, I'll tell the guys, I'm sure they won't have a problem with that." He started to walk away but stopped and leaned towards her. "But I won't be able to mask my good mood." He grinned and waggled his eyebrows and Elizabeth giggled. They walked together back to the group. Rodney begun dialing the address and John turned to Durai.

"Thank you for your hospitality. We'll see you in a few weeks."

"We will be looking forward to it. Farewell." Durai smiled and bowed while Elizabeth smiled widely. The team went through the gate and before John stepped through, he turned and smiled at Elizabeth, giving her a small wave.

It wasn't until a few weeks when John's team found Erentria almost destroyed.

* * *

TBC

Thank you for the feedback:)


	3. Chapter 3

John's heart thudded loudly in his chest at the sight. Some wooden houses were destroyed, lying on the ground as if they were cards blown away by wind. Some of the buildings seemed intact. Several roofs were on fire, though the rain that fell managed to extinguish some of the worst.

Naturally, his first thought was 'Wraith'.

Fighting back panic, his feet led him to only one place he could think of; Elizabeth's house. He entered the structure, which was more or less intact, calling her name desperately. Outside he could hear his team shouting, to see if there was anyone left. Calling her name again, all he got was a deadly silence. Moving from room to room he searched, stumbling over debris in his haste, but finding nothing.

With a knot in his throat he exited the building, squinting against the sunlight that beamed through the breaking clouds. The rain had extinguished all the fire and now all that was left was smoke coming from random buildings and big puddles of water on the ground. His team looked at him and he just shook his head.

"Durai! Elizabeth!" He called once again, knowing it was futile. She was gone.

"Colonel Sheppard!" He whirled at the voice and saw a young girl running towards him. It was Maya, her face streaked with dirt and a cut on her forehead as she looked at him with pleading eyes.

"Maya, what happened?"

"Colonel, please, you need to help us." She tugged at his arm and he followed, a spark of hope in his chest. He and his team ran after her, following her to a complex of caves. He entered the cave, spotting the villagers; some of the people were wounded and watched as Durai ran from one place to the other, tending to the wounded.

"Durai, what happened?" John approached him as Durai noticed him.

"There was a big storm, Colonel. According to our records, these types of storm occur only once in one thousand years. Will you please help us?"

"Of course." He nodded to his men and they began tending to the wounded. "Durai, have you seen Elizabeth?"

"Yes. She is over there." He motioned to the corridor around the corner. John started in the direction but Durai's hand on his arm stopped him. "She saved my daughter's life, Colonel." John nodded and felt his heart soar with pride. Anxiously, he went to the secluded spot where Durai indicated. Darkness filled the small enclave so he flipped on his gun light illuminate the area. To his horror it landed on two very still bodies, sheet draped over their forms.

That's when he heard a whimper to his left and he quickly swung his light toward the sound. Elizabeth. With a sigh, his shoulders slumped in relief, but concern drove him to move quickly to where she sat. Quickly he reached her side and crouched next to her, noticing first her blood coated. There was blood running down one side of her face as well, and he noticed a cut just below her hairline. Removing the flashlight from his P-90, he trailed the light downward in an effort to ascertain any other injuries.

The ray caught and reflected on something protruding from the material at her side and John froze. A small piece of metal was imbedded just above her hip and blood flowed freely from the wound. He reached careful hands to better assess the extent of the physical damage, only to have her slap them away. Then, with determined eyes, she took a hold of the shrapnel and pulled; it was all John could do not to flinch when the sickening sound of metal grating on bone filled the air. But with nothing more than a whimper, she extracted it the rest of the way and tossed it to the side, her shoulders now slumping in exhaustion.

"Jesus, Elizabeth..." He breathed. Releasing the breath he hadn't realized he'd been holding, he could do nothing but stare at her.

"Can you give me your field bandage?" Her voice shook him out of his haze and he immediately searched his vest. While she tucked her shirt up above the wound and he leaned in and pressed the bandage over it, trying to stop the bleeding.

"We need to get you a doctor."

"No. I'm gonna be fine."

"Elizabeth, no offense but you just pulled a damn piece of metal from your side."

"John, it's nothing, let it go. It will heal."

"Are you kidding? We're going right now."

"Have you forgotten I have nanites in my blood?" She spat out more angrily than she intended. He stared at her as if realizing it for the first time and then shook his head.

Remembering her other injury, his eyes snapped up to her forehead, and couldn't believe what he was seeing; the cut gash was weaving itself together until the skin appeared as if the cut hadn't been there at all. Elizabeth looked at him in confusion as he studied her and then she realized what he was witnessing. While he continued staring at her, she lowered her eyes and removed the bandage from her side. From the corner of her eye she saw John following her line of sight and he watched in rapt fascination as the tissue, muscle and skin creeped back together.

Sensing her uncertainty at his reaction, he grasped at levity, smirking, "What ever you're on, can I have some?" Elizabeth giggled and John chuckled with her. Pulling her shirt back down, she winced as she looked down at where the fabric was torn with large stain of blood around it. She shrugged and looked up at him

"Well, with your track record it would really come in handy." She grinned at him. He stood up and offered her his hand; she took it willingly and he helped her to stand up, surprising her when he embraced her tightly.

"I thought you were dead." He breathed into her neck and she smiled, hugging him close.

"I'm okay." She felt him nod and they parted reluctantly and walked back to the main cave to help the others. Major Lorne was first to notice her.

"Ma'am, are you alright?"

"Yes, I'm fine."

"What's with all the blood?" Ronon asked and motioned to her shirt and her stained hands.

"It's not mine." She wiped her hands against her skirt nervously. She turned back to John.

"How bad is the town?"

"Quite bad. Some of the wooden houses were completely destroyed, some roofs were on fire before the rain extinguished them but most of the houses are almost intact."

"We will need to rebuild." Durai joined their conversation.

"I'm sure a few Athosians can lend a hand or two."

"Athosians?" Durai asked with surprise. "I thought they were all taken by the Wraith."

"No, they are all safe. You know them?"

"Yes of course! They were our trading partners before the Wraith had been awoken again." John averted his eyes guiltily. "We would love to see them again. Halling, Jinto...and of course their leader, Teyla Emmagan."

"Well, that can certainly be arranged." John smiled and looked around. "But first, we need to get your wounded checked out by our doctors. Rodney, Lorne, get back to Atlantis and tell them of the situation, bring a med team with you." His two team members nodded and walked off.

"We should move the wounded back to the town."

"We should leave the people with worse injuries here, Keller needs to check if they can be moved." John suggested and they begun summoning the less injured people out of the caves and back to the town.

"Colonel," Dr. Keller approached removing her latex gloves, "most of the wounded will be okay in a few days, some cuts, bruises and minor burns. However, there are some with broken legs and one or two people with head injuries, I would like to take them back with me so I can make necessary scans."

"Okay, just tell me who and I'll go talk to Durai." Keller's head was turned and he noticed she wasn't listening to him. "Doc?" He called her but she didn't turn to him, so he turned his head and saw she'd spotted Elizabeth talking to Lorne nearby. "Listen, doc...I know it's a lot to ask but can you please not include this in your report? You know what they can do to her once they learn she's alive and here." Keller sighed and looked at him.

"Okay, Colonel. But I'll be accompanying the wounded back here once I'm finished and I'm going to perform a full scan on her. No arguments."

"Okay, you have a deal." He smiled at her and watched her approach Elizabeth with caution.

"Dr. Keller." Elizabeth eyed her warily and her eyes shifted to John.

"Dr. Weir."

"It's okay, Elizabeth. She won't tell anybody."

"As I said to Colonel Sheppard, under one condition; I'll make a full scan on you in two days."

"Okay." Elizabeth smiled. "That is acceptable."

Later, when Keller's team and John's team were walking back to the gate with the wounded, she turned to John.

"Now I know why you've been in such a good mood since you came back from your first mission here." She grinned at him and he smiled. The young doctor had noticed their military commander's improved disposition over the past few weeks and now she knew why.

He had found Elizabeth Weir.

* * *

TBC

You see that lil' purple button over there, yeh:D Thanks to everyone who reviewed so far, I hope you'll keep them coming. ;)


	4. Chapter 4

John stepped through the Stargate, leading the Eretrians to the infirmary. Ushering them through, he spotted Teyla with her baby at the top of the stairs, awaiting their return. Adopting a reassuring smile, he nodded, then proceeded to follow the rag-tag group to the medical facility. Once he was checked, discreetly scanned for nanites and given all clear, he went back to his room and took a long hot shower.  
Afterwards he settled down and grabbed his book, only to be distracted by the doorbell. He opened the door and saw Teyla with her baby boy and let them in, taking the toddler from the Athosian's arms; she smiled at him gratefully and sat down on the chair next to John's desk. He sat on his bed, the toddler in his lap, making faces at him.

"I hope this little tyke was good while I was gone."

"For once he has been calm and quiet." Teyla watched in amusement as her son gurgled at John and proceeded to grab his nose. "I gather your trip was not uneventful?"

"No, the town went through a huge storm that comes only once in one thousand years. Part of the town was damaged pretty badly. In fact, the day after tomorrow I'm taking some of the Athosians back with me to help with re-building some houses. I'll be helping them with my team, so we'll be staying a few days there. Durai would like to see you too." John bounced the toddler on his knee and the boy giggled happily.

"I would love to go with you, John."

"You can even bring Roi with you there too." He kissed child's forehead and continued bouncing him. "That is, assuming the doc gives you both the all-clear first. And there's a surprise waiting for you there too."

"What kind of surprise?"

"Nah, not telling. You'll see for yourself." John grinned and Teyla laughed when he tickled Roi, the toddler doubling over in laughter.

Two days later the big group arrived to Erentria, the wounded being welcomed back by their families, while the Athosians chatted amiably with other Erentrians, renewing old friendships. Dr. Keller excused herself, took her medical equipment, and disappeared into Elizabeth's house. John noticed but after spotting Durai, he waved the Erentrian leader over to him and Teyla with Roi in her arms.

"Teyla Emmagan." Durai beamed at her and kissed her cheek, placing a forehead against hers.

"Durai, it is good to see you again after so long."

"Likewise, my dear. And who is this little one?"

"That is Roi, my son." She beamed proudly and John left them to converse for a moment. A while later, Dr. Keller exited Elizabeth's house, wearing a soft smile.

"What's the verdict, Doc?"

"She's fine, the nanites in her bloodstream are still active enough to keep her alive."

"Is she dangerous?"

"No, as far as I can tell."

"Can I see her?"

"Of course. Go ahead." He walked inside of the house, spotting Elizabeth sitting at the dining table.

He greeted her with a smile. "Hey."

"Hi." She said shyly, rising from the chair, hugging him in welcome.

"Come with me, I have a surprise for you." He took her hand and tugged her towards him.

"What kind of surprise?"

"Now that wouldn't be a surprise if I told you, would it?" He grinned and she smacked his shoulder, but let him lead her outside.

"Elizabeth." It was a very familiar voice and both of them turned at the sound.

"Teyla." The expression on the younger woman's face was shocked mixed with happiness and relief. Elizabeth smiled at her widely and noticed the toddler in Teyla's arms; he was looking at Elizabeth with interest.

"This is Roi. My son." She said proudly and gently poked Roi. "Roi, this is Aunt Elizabeth." Roi extended his arms towards her and Teyla handed him to Elizabeth.

"Hi Roi." She smiled at the toddler, tickling him, pleased when he giggled. John watched the scene with a smile on his lips, glad his sunglasses were covering his eyes, otherwise they would all know how he was feeling just by looking at him. He pictured a child in Elizabeth's arms, with much paler skin and green sparkling eyes; though he knew it was never meant to be.

After they all dined together, Teyla with Roi and Keller bid them goodbye and returned to Atlantis. After the darkness fell and everyone went to sleep, John found Elizabeth on the patio at the back of her house.

"Couldn't sleep again?" He asked her from his spot in the doorway and she spun around to face him.

"Yeah. Too much has happened in the past few weeks...it's overwhelming." She smiled and looked at her hands clasped in front of her. He shut the door behind him and joined her by the railing. "Thank you for bringing Teyla here today."

"She deserved to know."

Elizabeth nodded and fought to keep her emotions in check. "I missed her. I missed you all so much." John took her small hand and gave it a little squeeze as Elizabeth looked up into his eyes.

"Show me."

"What?" She didn't understand what he was asking but when his hand tightened around hers, she knew.

"Show me. Show me what you've been through since then."

"No, no, John, I-I can't."

"Why?"

"I-I don't want to hurt you."

"You won't be sticking your hand in my forehead and I'll sleep off the headache." He shrugged nonchalantly and tried to lighten the situation. "It will be okay. Besides, I'm giving you permission to look and see what I've been through." He smiled at her and she smiled back nervously.

"Okay." He watched as she closed her eyes and concentrated, her hand squeezing his lightly. He closed his eyes...

...and then he stood on a beautiful beach, the sun was beginning to rise and he inhaled the scent of the sea. He opened his eyes and Elizabeth stood before him, dressed in white summer dress. The slight wind was rustling her hair and she smiled at him. He found himself smiling back before his gaze drifted down to where their hands were joined.

A bright light enveloped him and suddenly he was back at the Asuran home world at the time he was forced to leave her behind. He watched as the scene unfolded before him; her standing with her hand in Oberoth's forehead and John himself pointing his gun at them. Then Ronon dragged him away leaving Elizabeth in the hands of the Asurans.  
Even though he was observing from an outsider's standpoint, the pain of losing her drove a pang of loss through his gut. Next, he could feel Elizabeth leading him deeper inside; she let him feel her emotions and feelings, exposing herself completely to him. It was eerie watching his double and Ronon leave, feeling Elizabeth's relief when she knew they were safe. The determination inside of her was a tangible thing even though her own fate was now unclear; she refused to give up, she kept fighting.

Horrific memories and feelings displayed in his brain in thousands of colors, sounds and smells. He watched as she was taken to be experimented on by the Asurans, could feel her pain and also found out she was thinking about him all the time then. He watched as she refused to give the Asurans any information, was strong enough to resist their mind probing and could see their anger, frustration. He watched as they started attacking the Wraith hive ships, giving Elizabeth the opportunity to escape and that she did. They never realized she was gone because now all they could think of was killing the Wraith.

John watched in terror as Elizabeth was taken by the Wraith on another planet and he nearly screamed when the Wraith's hand was placed against her chest. Helpless to do anything, he could only watch as the Wraith pulled its hand back in confusion. Seconds later, its body started convulsing and John knew it was dead immediately. Beaten and bruised after her escape from the hive ship, Elizabeth finally found her way to Erentria, where she was taken care of by Durai and his wife, and weeks later she became a rightful citizen of the small town.

Elizabeth, on the other hand, watched as John landed the city on a new planet successfully, watched as guilt gnawed at him, for leaving her behind, for not helping her. She could feel his helplessness; saw his frantic desperation as he tried to find her. She watched through his eyes as Colonel Carter took command of the city and when Teyla told him she was pregnant. Elizabeth was relieved to find out John wasn't Roi's father, but some Athosian Elizabeth didn't recognize. She watched with a smile when the small baby was placed in his arms for the first time; saw how awkward and fumbling he seemed before he learned how to hold the small bundle.

She saw him fight, watched as he and his team were put in danger numerous times. As she probed his mind for more recent events, she saw the brief shocking return of Carson, and she felt a pang of sadness over their friend's demise. The most profound memory, however, was his love for her when he finally found her.

Easing them both from the tangle of their memories, they once again stood at the beach, their hands still linked, their fingers now entwined. She watched him open his eyes and look at her for a long moment, dozens of emotions playing across his face. Then he smiled and a bright light enveloped them both as she eased them back to reality; back to her back porch, back to Erentria.

They stood there in silence for a few minutes, still holding hands, not quite ready for separating from each other. If John didn't think they were close before, now they definitely were. This experience brought them much closer than he imagined, he never felt like that before, not even with Chaya when they shared their souls.

"The headache is not as bad as I thought it would be." He said after few minutes, reluctantly letting go of her hand.

"I tried to make it easier on you."

"Hence the beach, huh?"

She smiled at him when he turned to her. "Yes."

"Thank you, Elizabeth." He touched her arm briefly and she nodded, smiling slightly. The warmth of his hand left her arm as he stepped away from the patio and inside the house, closing the door quietly behind him. He needed to deal with what he had seen in her memories; had to deal with her feelings for him.

_Thank you, John. For showing me how you feel._ She thought and with a heavy sigh she continued to watch the night Erentria sky.

TBC 


	5. Chapter 5

The next few days were long and tiring as they all helped to rebuild parts of the town to its previous shine. John enjoyed all those simple tasks, being a part of a group, having fun together and it surprised him. It felt better than running around with his P90, chasing bad guys, or worse, being chased.

Not all of them were having fun though. John noted, with annoyance, how McKay was eyeing Elizabeth warily, putting as much distance between them as he could. While Rodney attempted to avoid her covertly, it was plain to John that she'd noticed and didn't say a word to any of them. He'd need to talk to McKay later in private.

Since the day of their 'connection', John noticed that Elizabeth no longer went to the back porch in the middle of night. John was a bit disappointed; he missed their nightly talks and being alone with her.

On the final night of his team's stay in Elizabeth's home, he rose from the sofa, padded silently to her bedroom door. Finding it slightly ajar, he pressed a hand to the wood and pushed it further open to peer inside. Elizabeth lay on her bed fast asleep, the sheet draped over her body. Entering the room, he closed the door softly and sat on a chair next to her bed, watching her sleep on her side, the expression on her face peaceful; the slow rise and fell of her chest and the sound of her breathing calming.

Just as he was almost dozing off, he nearly jumped out of his skin when he heard her soft voice.

"You going to sleep in that chair all night?" He dared to look at her; she was still lying on her side, facing him, her eyes now open, a soft bemused smile on her lips.

"I'm sorry, I didn't want to wake you."

"I wasn't sleeping when you came in."

"Then why didn't you say something?" he asked, clearly embarrassed to be caught.

"I like watching you squirm." She grinned at him and sat up. "Why are you here, John?"

"I went to see if you were sleeping. I wanted to talk." He smiled sheepishly at her and rubbed his hand across his face.

"Then by all means let's talk." She patted the spot next to her and he moved, sitting on the edge of the bed next to her, fiddling with the corner of the sheet. Elizabeth studied him for a moment with a smile on her lips when he fought for words he wanted to say.

After a few moments of silence, she nudged his shoulder playfully, "I thought you wanted to talk," she said teasingly. He looked up from his hands and found her grinning at him. He smiled and the tips of his ears burned with embarrassment. She shifted, so that she was sitting with her knees to her chest and her arms were wound around them.

"I went to see your mom last time I was on Earth." John finally offered.

"Yeah?" Her smile faltered at the memory of her mom and her throat closed with emotion.

"Yeah. I was in Washington for some meetings, so I thought I'd let her know. I really wasn't thinking, I was in my dress blues and..." He smiled at the memory of her mother's stunned expression when he'd turned up at her door. Nerves had caused his words to fumble then he'd attempt to assure her that Elizabeth was alive. "God, she thought you were dead when I showed up like that. She took it quite well...and I promised her to do my best to find you."

"And you did." Elizabeth smiled at him softly and he nodded with a smile and they sat a few moments in silence.

"Oh and Sedge adores me by the way." He grinned at her triumphantly and she burst out laughing.

"I thought she might." He watched her until her chuckles subsided, a small smile lingering on her lips.

The extremely tender but not unwelcome kiss he placed against her lips startled her. He pulled back slightly, studying her reaction before he leaned forward again and pressed his lips against hers, this time more boldly. They parted only when the need for air became critical, and Elizabeth smiled at him, her eyes twinkling.

"Hmm, you are very lucky, Colonel John Sheppard." The quality of her voice held a breathy sound and he tilted his head in silent question. "Her owner adores you too." He grinned broadly and kissed the tip of her nose playfully.

All his life McKay had found he needed little sleep. In a constant whirlwind of motion his mind craved activity and this night was no different. And, when McKay didn't sleep, a midnight snack was often called for, as it was tonight.

Exiting the kitchen, feeling triumphant that he'd made it through undetected by Sheppard, whom he couldn't see, but knew was asleep on the sofa, he held his slice of what passed for cake in this world and crept back upstairs. An odd sound reached his ears and he froze.

Peering into the darkness of the room he realized it was the sound of Elizabeth's bedroom door opening. He crouched silently behind the railing and saw John standing in the doorway, his hand rising to caress Elizabeth's cheek lovingly. He watched John smile and kiss her lightly, before she bid him goodnight and closed the door behind her. As John returned to the room, Rodney crouched lower and stared as John lay back down on the sofa, covering himself with the quilt and fell asleep. The astrophysicist went quietly upstairs, knowing he would need to have a word with the city's military commander.

The next morning as they were packing up and ready to leave, he found John alone inside the house, zipping up his vest. He approached him and cleared his throat.

"Colonel, can I have a word with you?" John lifted his head and raised an eyebrow.

"Sure. What's up?"

"I wanted to talk to you about Elizabeth."

"What about her?"

"I saw you."

"What do you mean?"

"I saw you, last night, when I was on my way back from the k…er… bathroom."

"And?"

"I saw you two kissing."

"And? McKay, get to the point." John was quickly losing patience. He knew the scientist was a bit in love with her, but surely he wasn't jealous. Or was he?

"That," Rodney hissed angrily, "was the most stupid and reckless thing you've ever done."

"Excuse me?"

"Touching her. Kissing. And…God knows what else you've been doing over the past few days."

"McKay, that's none of your business."

"The hell it isn't!" Rodney's voice snapped loudly. He quickly lowered it to keep from attracting attention, "You completely disregarded what I told you! You have no idea what she can do to you! You are endangering the mission!"

"McKay, Keller said-"

"Keller doesn't know everything."

"Oh and you do?"

"Elizabeth is not your friend anymore. She's the enemy." If John hadn't spotted Elizabeth standing in the doorway of her room across the house behind Rodney's back, he would have punched the scientist. He didn't know how long she'd been standing there, but from her hurt expression he knew she heard most of it.

Rodney noticed John's lack of response and how his eyes focused on a spot just over his right shoulder. He turned to follow his gaze and his face fell instantly. Elizabeth stood there, her eyes touched his momentarily then dropped, utterly crushed. Then, she spun on her heel and disappeared back to her room.

"Get out of my way, McKay." John pushed his way around Rodney and followed, shutting the door behind him. She was sitting by the window, looking outside at the small backyard and his chest hurt at how sad she seemed. He crouched beside her chair, gently touching her thigh.

"'Lizbeth, I'm sorry you had to hear that." She looked down at him silently. "McKay's an idiot."

"He's right." She spoke softly and quietly.

"What?"

"I haven't given any of you reason to trust me."

"Elizabeth, I trust you with my life." He caressed her cheek softly. "We all trust you. And if McKay doesn't, that's his problem." He lifted her chin with his finger to make her look at him.

"Don't worry about it. Now, c'mon and tell your flyboy goodbye properly." Elizabeth rolled her eyes and let him tug her up to standing position. She looped her arms around his neck and kissed him lightly.

"When will I see you again?" She asked when they parted, breathless.

"I don't know. As soon as possible, I promise."

"Okay." She smiled at him softly and brushed her lips against his again.

Colonel Carter waited for John's team and several Athosians to return through the Stargate. Surprised, she looked closely at McKay when they stepped through the event horizon. He was sporting a rather large black eye. She looked at John with raised eyebrow, getting a muttered response as he stalked away, his expression unreadable, though his eyes were hard and cold.

"Minor disagreement," he muttered exiting the control room. Looking for more explanations, she looked at Rodney.

"What he said." McKay pointed after John and walked towards the infirmary. Carter could see he was acting very un-McKay like, so as last resort, she looked at Ronon and Lorne, but they only gave her a mere shrug. Sighing, she pinched the bridge of her nose and went back to her office.

A few hours later John stood in said office in front of Carter's desk as she pierced him with a glare. John never really liked her, not because she took Elizabeth's job, that wasn't her fault, she had had her orders. No, his dislike stemmed from that fact that to him it seemed she tried too hard to get on with everybody and eventually, that drove him away.

"I don't know what your argument with McKay was about, but I hope it won't get in the way of how you work off-world, Colonel. The last thing I want is to get one of you transferred to a different team, so I hope you have already worked out your differences." His face was expressionless as he just stood there, his hands behind his back.

Her face and her voice softened. "John, I know that this year has been crazy. The loss of Dr. Weir has been hard on us all, but eventually, you will need to move on, put it behind you. Accept the fact that you may never find her. She might not be alive anymore. I'd like you to talk to Dr. Heightmeyer; she can help you deal with it." She looked at him, his face still expressionless, his posture as stoic as ever. She sighed. "Dismissed." He started for the door but paused.

"Ma'am?" She looked from her paperwork to see him hovering in the doorway.

"Yes?"

"Next time I'd appreciate if you addressed me with my rank." With that he was gone. Carter, stunned and surprised, only stared at his back as he exited the control room.

A couple weeks later an unsuccessful mission landed him to infirmary, effectively trapping him down to bed rest for two weeks, thanks to a broken leg and clavicle. It had been more than four weeks since he'd last seen Elizabeth and he missed her terribly. His mood was darkened further when he heard Teyla came to visit and announced that she was to go to Erentria to visit friends and observe how the crops were doing after the storm destroyed them.

Sitting on the uncomfortable infirmary bed, he shifted but spied Keller approaching to change the dressings and he sighed like a sulky, petulant five year old. Teyla looked at him with a patient smile and leaned forward to whisper:

"Do not worry," she said with a patient smile, "I will greet her for you."

"Thanks," he offered. But he'd rather do that himself so he watched her leave and resumed his pouting. Dr. Keller came around the corner and once she saw his fallen expression, she let out a heartfelt laugh and began changing his dressings.

"What's the matter with you, Colonel?"

"When can I go back on duty, doc? This is pure torture."

"Well, if you hadn't been so clumsy on your last mission, you wouldn't be here."

"It's not my fault those bad guys decided to ambush us." He winced when she ran her fingers across his broken collarbone, checking how it was healing.

"Of course not, but I thought you were old enough not to trip over stuff." John growled and Keller laughed again, leaving him on his own.

With a heavy sigh, he managed, albeit with some difficulty, to lower to the floor, take his crutch and awkwardly hobble off to his quarters. Once arrived, he collapsed on his bed, then, taking his book, War and Peace, he sighed and turned to page 254. Half an hour later he became bored with the book and tossed it away, finally dozing off.

The sound of the city's warning chimes jarred him awake. Incoming wormhole, he knew by the alarm, and within minutes the sound died off. Frustrated, John ran a hand through his hair; it was annoying not to know what was happening. Well, it couldn't hurt to just ask, so decided he crawled out of the bed, hobbled to the door, only to nearly collide with Dr. Keller once in the hallway.

"Whoa." John grabbed her arm to prevent her from falling and leaned against the wall to balance himself. "Why the rush, Doc?"

"Teyla radioed in a few minutes ago, saying that one of her friends on Erentria passed out. She seemed rather distraught." John's brows furrowed. "If you excuse me, I should be back soon." He nodded and watched in concern as she hurried away, a feeling of dread twisting painfully in his gut.

Knowing he wouldn't be able to get any sleep until he knew more, he returned to his quarters, sat at his desk and started working on the backlog of paperwork and mission reports. Later he checked his watch, noticing it was almost two hours since Keller left. He stretched a bit, wincing at the pain in his shoulder, then scrubbing a hand across his face, he decided to have early dinner. However, he was interrupted by a doorbell of his quarters.

"Come in." He called and the door swooshed open, revealing Dr. Keller. Something told him this was bad. "Doc?" He sat up straighter as she entered, the door sliding shut behind her.

"I just wanted to tell you that Teyla and I were back." But there was something else in the way she stood chewing on her lower lip, as if she were trying to find the words.

"Is everything okay on Erentria?" God, that gut twisting dread returned and when she shifted uneasily after that question, the feeling tripled.

The physician sighed and nodded, "Teyla was purposely vague when we got her message earlier." She swallowed and continued, "John, it was Elizabeth who passed out."

"Is she okay?" Panic laced his voice and if Keller noticed, she didn't comment on it.

"She's okay, Colonel. She just needs plenty of rest now." She paused. "You realize I shouldn't be saying anything to you about her condition under normal circumstances." She waited until John nodded hesitantly; and if she was correct in her assumption, he had a right to know.

"Colonel, she's pregnant."

TBC

* * *

Thanks for the alerts and reviews! I don't know why but the editor always strips away all my separators from the fic which separate parts indicating some time has passed in between. Help? 


	6. Chapter 6

Two days later John was more mobile and accompanied by his team stepped through the gate to return to Erentia. This trip, they brought Roi, bundled tightly in Teyla's arms, Dr. Keller rounded out the group. The cool air announced the arrival of the planet's fall season.

While still on the mend in Atlantis, John had been adamant about making a return trip back to the planet as soon as possible, despite his less than ideal physical condition. With one arm still in a sling, he relied heavily on the use of a crutch with his good arm to support his still healing leg. During their briefing, prior to departure, John was well aware of how closely Colonel Carter scrutinized him and he didn't blame her. However, he didn't care; with a sudden feeling of urgency he needed to see Elizabeth, needed to make sure she was okay.

Stopping, John hitched up his collar against the chill of the air, and after adjusting his hold on the crutch, he began walking towards the village, the team behind him. So intent on his destination John didn't notice Rodney cresting the top of a small hill on his way back to the village. He'd arrived days earlier to study some Ancient ruins they'd stumbled on a previous visit.

Not long after they reached the small settlement, Durai and his wife, Ilithyia, greeted them warmly. Reacquainted friends, Ilithyia and Teyla immediately struck up the conversation while Durai's wife quickly embraced Roi. It was clear that she loved children; after all she was a midwife. With a nod to John, Teyla and Ronon followed Ilithyia to her house, chatting amiably. John and Dr. Keller excused themselves and went to the direction of Elizabeth's house.

* * *

Rodney McKay walked quietly into the village. He'd heard that his team was coming to the planet today so he'd returned to the village from the ruins to meet up with them. However, spying a still-injured Sheppard amongst the group was not what he'd expected and he slowed his pace to watch as his people dissipated and went their separate directions.

"Huh," he huffed quietly, looking in the direction of Sheppard and Keller. His eyes narrowed questioningly and his brow furrowed. "What's Keller doing there?" he asked more himself than Durai but the councilor answered him anyway.

"Oh, I thought you knew. Elizabeth is with a child." A beaming smile appeared on Durai's lips. Rodney's face showed disbelief but Durai didn't notice.

"What?"

"We are all so excited; we haven't had a single birth in the town for many, many moons."

Rodney swallowed the sharp retort and mumbling to himself, he left a very confused Durai standing there all alone, heading for the ruins.

Rodney knew what he had to do. He only hoped they would forgive him.

* * *

"I'll make a quick check-up on Elizabeth, and then you can see her." Dr. Keller paused in front of the bedroom door. "I was planning on doing an ultrasound later." John acknowledged this with a nod and watched as the young doctor disappeared inside the bedroom and sat on the sofa. Ten minutes later Keller emerged from the bedroom with a small smile on her face, holding a small vial of blood in her hand.

"You can go in, Colonel. I'll just run a few tests on her blood, and then we can do an ultrasound." She moved to the kitchen table to begin setting up the appropriate medical equipment.

John nodded and hobbled towards Elizabeth's room only to stop halfway and turning to look at Keller, "Doc?" He hesitated a moment as the doctor raised her eyebrows in encouragement. "Does...does the baby have nanites?"

"It's too early to tell, Colonel. I will need to take some samples when the fetus is more developed." She paused. "I guess it could be compared to HIV in terms of passing the nanites to the baby. The risk of getting infected is about 20 to 45 percent. There's no way to know for sure yet."

"Thanks, Doc." John nodded and let Keller do her work while he knocked on the door. Hearing Elizabeth's faint 'come in' he let himself in, smiling when he spotted her lying in bed. She looked at the newcomer and her pale face lit up with a smile and she struggled to sit up.

"John! What are you doing here?" She eyed him suspiciously, and then noticing his condition her gaze narrowed.

"Can't I just drop in to see you?" He grinned and sat on the edge of her bed, placing the crutch against the frame. He placed a small kiss on her lips, feeling her smile.

"Keller told me you were ordered to bed rest. So no, no you can't." She eyed his splinted leg and his arm in a sling. "What happened to you?"

"Y'know, same old. Being chased by evil people..." Elizabeth raised an eyebrow. "Ok, so I tripped when they chased us." He winced and Elizabeth tried to hide her amusement. He narrowed his eyes at her and her grin widened. His expression softened and looked into her eyes. "But I'm not here to talk about me." His eyes strayed downwards to her stomach and then up to her face again. She was biting her lip and smiling ever so softly. His hand reached out tentatively, and rested on the spot where he knew the baby was growing inside of her.

"When Keller told me, I couldn't quite believe it." He said after a while, his finger caressing her belly. Her hand covered his and squeezed, their fingers intertwining as he rested his forehead against hers.

"We should have been more careful." She let out a low chuckle and he kissed her forehead.

"Yeah, but I'm not regretting it."

"Me neither." They smiled at each other before John leaned in and captured her lips in a sweet kiss that grew needy; neither of them heard the soft knock on the door. It wasn't until Keller stepped into the bedroom they jumped apart.

The young physician smothered a grin, adopted an apologetic smile and offered, "I'm sorry, I didn't want to interrupt."

"It's okay, Doc." John smiled and Elizabeth blushed. "What did you need?"

"I was thinking of doing the ultrasound. I forgot some of my stuff back on Atlantis so I will need to take the blood sample back with me to run tests on it." Seeing them both nod, she moved entirely into the room, placing the small portable ultrasound on the bedside table. Elizabeth hesitated but then lay back down on the bed, lifting her shirt and wiggling the waistband of her pants down to her hips, exposing her flat stomach.

John knew it wouldn't be flat much longer and his eyes drank in the sight of her. Her hand found his unconsciously while Keller placed the scanning device on Elizabeth's gel-covered abdomen. John's eyes remained glued to the screen, searching for their baby.

"Ah, there it is." Keller drew their attention to the screen after several tense seconds. Both John and Elizabeth squinted at the screen and they saw...nothing. Seeing their frustrated faces, the young doctor smiled and zoomed in on the area. John looked closely at the monitor and that's when he saw it.

Keller pointed to the screen and a small black circle, adding, "This is the gestational sac and this..." she zoomed in a bit again and pointed to the small shape inside the circle. "This is the fetus pole." She described the tiny shape.

Before she could say anything else, John spotted small fluttering and he knew; it was the heart of their baby. It was smaller than an inch but it already had a heart. John couldn't tear his eyes away from the screen; in the back of his mind he registered Elizabeth's hand tightening around his.

"From the size of the fetus," she continued, "I can assume it's six weeks old, give or take. It appears to be growing without any problems, the heart rate is okay too." She removed the device and handed Elizabeth a few tissues to wipe her stomach with. Turning off the machine, she added. "We'll be making more scans throughout your whole pregnancy and generally keep an eye on you, just in case. Congratulations."

"Thank you, Doctor." Elizabeth shifted so now she was again sitting with her back propped against the headboard. "Am I going to feel this exhausted all the time?"

"It should pass in a few weeks. Other than that, do you have any problems? Nausea? Dizzy spells? Cravings?"

"All of them." Elizabeth grinned. Standing up, Keller found herself smiling back.

"Those will pass too over time. Just keep taking the prenatal vitamins I gave you and take it easy." She nodded to both of them and left the room.

"Cravings, huh?" John grinned at Elizabeth and kissed her forehead.

"Yes. Promise you'll bring me some peanut butter next time."

"You got it." He chuckled and winked at her before dipping down to steal one small kiss.

It was evening when the team gated back to Atlantis, pleasantly sated after a generous dinner, which Durai and his wife prepared for them. Rodney stared defiantly ahead, his back towards the parting couple. John kissed Elizabeth softly and then pulled her into his arms, his fingers curling in her hair.

"I'll be back before you know it." His warm breath washed against her forehead and she smiled.

"You better be, I want my peanut butter." She smiled at him and withdrew from his arms. His fingers lingered for a few seconds where their baby grew and he smiled, and with one last look he stepped through the event horizon.

* * *

Few days later

"Colonel, ah, I've been looking for you." Dr. Keller called out to John as she saw him passing by the infirmary. He stopped and made his way over to her and she motioned him to a more secluded area of the infirmary. His chest tightened.

"What's up, Doc?"

"I've completed the tests on the sample of Dr. Weir's blood." She paused and bit her lip, unsure of how to continue. "I checked three times to be sure and compared the sample to the ones we've had here when we decided to heal her with the nanites." She exhaled and tried to deliver the news as gently as possible. "The amount of nanites in the recent sample is significantly smaller than in the other samples. When I took her blood six weeks ago, I didn't notice anything amiss. However, if we don't stop the nanites from deteriorating, we will lose her, Colonel."

TBC

* * *


	7. Chapter 7

John swallowed a few times and Keller watched him as he processed the new information. Running a hand through his hair, he began to pace.

"Why is that happening?"

"I have no idea. This is why she's feeling so exhausted most of the time."

"How long does she have?"

"At this rate, I'd say a few weeks." She put a comforting hand on his shoulder. "I'm sorry." John dropped his head and closed his eyes. He didn't find Elizabeth just to lose her again. There must be something they could do; he wasn't going to let some stupid micro robots take her and their baby away.

"Is there anything we can do?"

"Until we determine what's causing the deteriorating, we can do nothing but guess." They walked the length of the infirmary and into Keller's office. "I need to run more tests, I'm going to have to go back to Erentria to get more samples…and inform her of what's happening."

"Ok, I'm going with you."

"You aren't going anywhere, Colonel Sheppard." A familiar voice from behind them made them jump. Closing his eyes for a moment, he wondered how much she had heard before he turned around, a defiant look on his face.

"Dr. Keller, you may return to Erentria." Colonel Carter continued and Keller nodded, gathering her things and some nurses. "I'd like to talk to you, Colonel. In my office please." John swallowed the sharp retort that it wasn't her office and obediently followed. The tension between them was obvious as they walked in silence to their destination. Once arrived, Sam walked around her desk, arms folded in front of her, anger and disappointment evident on her face. John suppressed the urge to shift.

"Colonel, would you mind telling me what business you have on Erentria?" John visibly cringed at the word 'business' but looked at her in feigned confusion.

"With all due respect, I don't know what you're talking about, ma'am."

"Oh, I'm sure you know perfectly well what I'm talking about, Colonel." She spat out angrily. "I have been informed about what has been happening on Erentria, so you can drop the act." John lifted his chin a bit and put his hands behind his back, staring defiantly on the spot on the wall behind her shoulder.

"I would like to know why you forged your mission reports and forced your team and the medical team to do the same."

Knowing full well there were only a few people who had known of the recent happenings on Erentria and John just couldn't believe one of them betrayed him and Elizabeth. He knew it wasn't Teyla, Ronon, Major Lorne or Dr. Keller, so that left the one person who was most uncomfortable with Elizabeth's presence..._I'm going to kill that son of a bitch_.

"I haven't forced anyone."

"According to my source, you ordered them not to say a word to anyone."

"You can drop it, Colonel. I think I figured it was McKay who spilled the beans to you."

"Don't blame him for this, Colonel, he was just concerned about Dr. Weir." John snorted and Carter narrowed her eyes at him.

"Concerned? Oh please, McKay is always only concerned about his own ass."

"Colonel, that is enough!" She bellowed and the whole control room stared at them. She went to close the door and approached John, standing directly in front of him, so he didn't have a choice but to look at her.

"It was completely reckless to get into direct contact with Dr. Weir, let alone being in…intimate relationship with her." John's eyebrow quirked but he didn't say anything. Carter sighed. "Every action has its consequences. I know you meant well with protecting Dr. Weir, Colonel. However, I have my orders. Colonel Sheppard, as of right now you're under custody."

John froze on the spot. "Why?"

"Our superiors deem it necessary. You will now be escorted to the brig." She stated with a nod to the security guards who had just entered the room. "Later today you will be escorted back to Earth, where the IOA will conduct an interrogation with you." Two large hands clasped around his arms and he futilely tried to shake them off. "Dismissed."

The guards led him away, through the maze of corridors, the passing Atlantis personnel watching in confusion. John stopped when he spotted McKay and the guards nearly collided into John's back. McKay had the grace to look bewildered.

"Happy now?" John snarled and McKay backed away a little. "Got what you wanted, huh?" Fearing the Colonel's rage would give way to an open attack on the scientist, the guards grasped his arms firmly and led him away, leaving shocked McKay behind. This was not what he wanted at all.

----------------------------------

Later that day, thanks to the midway station, he found himself back on Earth at the SGC, being interrogated like the worst criminal, and the same questions being asked over and over again. He slouched in one of the chairs, his arms folded in front of his chest, looking at the IOA representative across the table.

"Why have you not included your encounter with Dr. Weir in your mission reports?"

"She asked me not to and I respected her wish."

"Why? Colonel Sheppard, Dr. Weir is still under the influence of the replicator nanites and by being in contact with her, you were endangering your team and risk divulging the city's current location to the Wraith and the Replicators." John fought the urge to roll his eyes and he decided he didn't like this guy much. Just like the rest of the IOA, Woolsey be damned.

"Dr. Keller said she was not dangerous."

"Not even Dr. Keller can determine the imminence of the microscopic robots inside Dr. Weir."

"Dr. Weir hasn't made any act of aggression towards us in the past 3 months. She told me what had happened in the past year, and I believe her. I trust her with my life."

"You may not know of any acts as of yet but they could still be happening."

"Oh I see. Guilty until proven innocent." John shook his head and before he could say anything else, he got interrupted.

"This report says you have had rather intimate relations with Dr. Weir while she was still under the influence of the nanites, resulting in Dr. Weir's pregnancy. Is that correct, Colonel Sheppard?"

John made a noncommittal sound; they already knew that without his confirmation, so he didn't bother.

"You have put yourself and others in danger by coming into close contact with Dr. Weir, Colonel."

"You don't know that for sure."

"You could have been infected with nanites!"

"But I wasn't!"

"It was the most reckless behavior, Colonel!" The IOA's representative questioning him stood up abruptly and placed his hands on the table, leaning towards the Air Force pilot. With a defiant tilt of his chin, John moved to mimic the interrogator and pushed his chair back, but before he could finish the blaring sound of the klaxon interrupted, announcing an incoming wormhole.

John watched as Walter bounded up the stairs to the briefing room. After whispering something to General Landry, he then went back down to the control room. General Landry, who had been just a quiet observer of his interrogation, suddenly spoke up.

"I'm sorry gentlemen; I'll have to interrupt this briefing. Colonel Sheppard, Atlantis is dialing in, Dr. Keller wants to talk to you, and she says it's urgent." At the mention of Keller's name, John's heart started pounding and the feeling of dread suddenly overwhelmed him. He raced down the stairs, just in time to catch Keller on the screens.

"Doc, what's wrong?"

"Colonel, we've found out what's wrong with Dr. Weir."

"Really?"

"Yes." She smiled and explained it all to him.

A few minutes after the talking with Keller, John returned to the briefing room. The IOA representatives were talking amongst themselves. He cleared his throat and they looked at him expectantly.

"I have a proposition for you."

TBC


	8. Chapter 8

After more talks, John returned back to Atlantis a few days later. Colonel Carter greeted him when he stepped inside her office but he only replied with a curt nod and a grim expression on his face. In confusion, she watched as he threw a folder on her desk with a loud slap. Cautiously she retrieved the document and opened it, the contents revealing several sheets of paper. Taking a moment, she skimmed the pages then lifted her gaze, eyes wide, surprise clearly in her face.

"The IOA want you to read this and sign it eventually, Ma'am. With your permission I'd like to stop by in the infirmary for a check up."

"Y-yes, of course. Dismissed." He gave her a nod and stalked away. She sat heavily in her chair and spread the papers in front of her. This was going to be a long day, she thought, when her eyes took in the first paragraph. This decision would change many lives.

John's mood improved slightly as he went through the corridors to his destination, the crewmembers were greeting him warmly and he had to smile. These people were genuinely happy he was back. He rounded the corner and spotted two guards outside the infirmary. He studied them carefully and then entered, freezing right on the spot.

"Elizabeth..." He whispered and rushed to her bedside. She was reading a book and looked up when she heard footsteps.

"John." Setting aside the book, she sat up straighter. She was pale, very much so, and his forehead creased in worry. He sat on the edge of the bed and took her hand, gently kissing her knuckles.

"What are you doing here? Did they bring you here by force?" Rage welled within him but it was wiped away when she shook her head and placed her other hand on his cheek.

"No, nothing like that. I was bleeding. Dr. Keller had to bring me here for a full check up."

"Are you okay? Is the baby...?"

"We're okay, don't worry." She smiled and placed a small kiss to his lips. Just then Dr. Keller rounded the corner and smiled at them.

"I see the rumors all around the city are true. Welcome back, Colonel."

"Thanks, it's good to be back."

"Since you are here, I can tell you in detail of what we discovered." The couple nodded and Keller pulled up a chair and started speaking. "This came to me when I was comparing the baby's DNA to yours, Colonel. It's a standard procedure; we learn how the ATA gene is passed on. Now, we know that the Replicators are prevented from harming their creators...the ancients with the ATA gene."

"But I don't have the ATA gene, the therapy doesn't work on me."

"Yes, but the baby does. The nanites in your system are pushed away by the baby's gene. Your body refuses the gene therapy but it doesn't refuse the baby. The genetics here call it the nature's intervention; basically it is making sure the strongest gene carriers will survive even in less ideal surroundings. That way it ensures the gene is passed on for many generations."

"The baby is healing me?"

"Basically, yes."

"So what happens when the baby is born then? Will she die?"

"No, we have discovered that once the baby is born, there is a small gene marker on the mother's DNA that stays there forever. It's not enough to operate the technology but in this case it's enough to keep Elizabeth alive."

"Wow."

"Yeah."

"If I had known this would heal you, I'd have jumped you a year ago." John grinned cheekily and Elizabeth narrowed her eyes at him. Laughing, Keller stood and put the chair back in its place.

"I'll leave you two, I'm sure you have a lot to talk about."

Once she left, John leant in, giving Elizabeth a gentle kiss. She pulled back suddenly, biting her lower lip. He knew she had something on her mind but didn't know how to tell him. He nudged her slightly.

"What is it?"

"Rodney came by earlier." John tensed and his lips narrowed into thin line, his hands fisting at his sides. Elizabeth sighed. "John, you need to forgive him."

"Forgive him? He all but treated you like some disease, Elizabeth. He gave us up."

"They would have found out eventually, it was just a matter of time. He explained to me why he did it. Rodney cares, John. He might have a weird way of showing it, but he cares about us. He never thought it might get you in trouble. He just wanted to help."

"You were there, Elizabeth. He called you the enemy. That's a pretty warped way of showing he cares."

"You know how he can get, John. He apologized for it. He was afraid, and had every right to. For all he knew, I could have been double-crossing you; you had no idea if I was completely overtaken by the nanites. Tell me, would you be so trusting if it was someone else? If you didn't have feelings for them? You let your feelings cloud your judgment, John."

"Oh, so now it's my fault?" He looked at her in disbelief and stood up from the bed, running a hand through his hair. Elizabeth sighed heavily and rubbed her forehead, knowing that this was one of the times John Sheppard was being impossible.

"No, I'm just trying to make you understand why Rodney did it. And yes, while he should have spoken to you first about it, he actually did us a favor." John stopped his pacing and turned sharply to face her.

"Are you kidding me? He almost put you under a microscope! And you would have ended up there if I hadn't persuaded them to leave you alone." He turned his back to her, his feelings in turmoil. Elizabeth watched; with his posture tense and his shoulders rigidly straight she realized there was something else he wasn't saying.

"What did you do?" She asked, her voice hard. No reply came, so she asked again. "What did you do, John?"

He replied quietly after several seconds of silence.

"I left the Air Force."

----------

Expecting an angry outburst, he turned and looked at her. Instead, she was there sitting and staring at him in silence. Outbursts he could handle, but silences were something different altogether. She blinked several times and then closed her eyes momentarily, turning her head away from him.

"Why?"

"Elizabeth..."

"Why did you do it?" John sighed and sat back on the bed, making her look at him.

"So I could be with you. I'll do anything to protect you, Elizabeth. The both of you."

"What about Atlantis?"

"They will replace me. Besides, we're allowed to visit every now and then. We can choose; stay in Pegasus Galaxy or go back to Earth."

"I'd like to stay on Erentria. Life there is...easier. Simpler. But what about you?"

"What about me?"

"I don't want to keep you from anything. I don't want you to become bored after several months there."

"I won't. Right now I'm pretty excited." He placed his hands on her covered belly and smiled. "And that's not going to change anytime soon." He said, already imagining their lives with this little one and one or two more children. Elizabeth smiled at him and bit her lip, clasping his hands in hers.

"I have a request, though."

"What is it?"

"I want to see my mom."

----------------

Two months, one last trip to Earth and back and two weeks since Elizabeth moved her things to Erentria, John exited the wormhole on his new home planet. Saying goodbye to his friends was hard, but he knew he would see them again and in short time. In only a few months their child would be born, and his team promised to visit then.

Before leaving, John did forgive Rodney, and in the last two months, they talked about it several times. Through their discussions he came to realize the scientist had meant well, but anger clouded his judgment then and he'd been unable to see that. Now, however, with everything settled, he felt lucky to have friends like that.

John breathed deeply through his nose, taking in the smell of the fresh air on Erentria. This was his home now. One chapter of his life ended, while another, more exciting, was just beginning.

THE END

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Thanks to those who reviewed so far, I really appreciate the feedback:) 


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